Random Amplified Polymorphic DNA (RAPD) using PCR
In the last topic, polymerase chain reaction(PCR) was described which has revolutionized molecular biology research. If primers with arbitrary sequences (random primers) are used for PCR amplification, DNA segments to be amplified will be selected at random which will thus provide a truly random sample of DNA markers, which are described as random amplified polymorphic DNA (RAPD = pronounced as 'rapid'). An example of RAPD markers demonstrating genetic diversity in maize genotypes is shown in Figure 40.9. RAPDs have several advantages over RFLPs and can be used as their substitute in several studies. The main advantages include the following : (i) since same primers with arbitrary sequences can be used for different species, no species specific probes are needed for different species as required in RFLPs. For instance, primers that provide polymorphic markers in maize, also provided polymorphic markers in soybean, Arabidopsis, humans, Neurospora, etc. (ii) collection of data using RAPDs proceeds much more quickly than those using RFLPs, since there are fewer steps involved (Table 40.2). It has been shown that generation of RAPD data is five times quicker than RFLPs.

Fig. 40.9. Random amplified polymorphic DNAs (RAPDs) in maize.

RAPD technique may also be combined with RFLPs to increase the efficiency of molecular markers for genetic analysis. A RAPD marker known to be polymorphic may be labelled and used as a probe for RFLP analysis, thus eliminating the need for recombinant DNA cloning of probes in bacteria.